Removal of extraneous ports, removal of perseus-web, disable traefik …

…dashboard Add MAVEN_PROFILE to webapi-from-git pattern
OHDSI · Jan 5, 2024 · e2aa50a · e2aa50a
1 parent a593585
commit e2aa50a
Show file tree

Hide file tree

Showing 8 changed files with 170 additions and 140 deletions.
diff --git a/.env b/.env
@@ -220,6 +220,7 @@ ATLAS_GITHUB_URL="https://github.com/OHDSI/Atlas.git#1297c137669f21babace1906f23
 
 # if building WebAPI from git rather than docker hub image
 WEBAPI_GITHUB_URL="https://github.com/OHDSI/WebAPI.git#rc-2.13.0"
+WEBAPI_MAVEN_PROFILE="webapi-docker" # Set this to webapi-docker,webapi-solr if you want to enable SOLR Vocab search
 
 ############################################################################################################################################################
 # Section 7:

diff --git a/.github/workflows/perseus.yml b/.github/workflows/perseus.yml
@@ -35,4 +35,6 @@ jobs:
       - name: Build perseus profile
         run: docker compose --profile perseus up -d
       - name: Test perseus frontend
-        run: curl -s --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/perseus/sign-in
+        run: |
+          sleep 30
+          curl -s --retry 10 --retry-connrefused ${{matrix.httpType}}://127.0.0.1/perseus/sign-in
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,4 @@ phoebe/concept_recommended.csv
 phoebe/__MACOSX
 atlas/add_cdm
 .Rproj.user
+strategus/
diff --git a/README.md b/README.md
@@ -232,6 +232,8 @@ The Broadsea atlasdb Postgres instance is listed by default, but you can use an
 
 #### Build SOLR Vocab for Atlas
 
+**Note: with WebAPI 2.14, you will need to use the webapi-from-git profile and set WEBAPI_MAVEN_PROFILE to webapi-docker,webapi-solr**
+
 To enable the use of SOLR for fast OMOP Vocab search in Atlas, review and fill out Section 7 of the .env file. You can either point to an existing SOLR instance, or have Broadsea build one. The JDBC jar file is needed in the Broadsea root folder in order for Solr to perform the dataimport step.
 
 ### OHDSI Web Applications

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -98,6 +98,7 @@ services:
       context: ${WEBAPI_GITHUB_URL}
       args:
         MAVEN_PARAMS: -DskipTests=true -DskipUnitTests=true
+        MAVEN_PROFILE: ${WEBAPI_MAVEN_PROFILE}
     extends: 
       file: "./compose/ohdsi-webapi.yml"
       service: ohdsi-webapi
@@ -214,22 +215,6 @@ services:
       - ./phoebe:/tmp
     entrypoint: ["sh", "/tmp/load_phoebe.sh" ]
 
-
-  # broadsea-arachne-execution-engine:
-  #   profiles: [ "arachne-execution-engine" ]
-  #   build: ./arachne
-  #   container_name: broadsea-arachne-execution-engine
-  #   restart: unless-stopped
-  #   ports:
-  #     - "8888:8888"
-  #   privileged: true
-  #   platform: "linux/amd64"
-  #   volumes:
-  #     - ./execution_engine:/dist
-  #   labels:
-  #    - "traefik.enable=true"
-
-
   # Security providers for testing purposes
 
   broadsea-openldap:
@@ -260,7 +245,7 @@ services:
     platform: "linux/amd64"
     container_name: broadsea-open-shiny-server
     restart: unless-stopped
-    ports:
+    expose:
       - "3838:3838"
     volumes:
       - ${OPEN_SHINY_SERVER_APP_ROOT}:/srv/shiny-server/apps:ro
@@ -273,7 +258,7 @@ services:
     platform: "linux/amd64"
     container_name: broadsea-posit-connect
     restart: unless-stopped
-    ports:
+    expose:
       - "3939:3939"
     privileged: true
     environment:
@@ -333,12 +318,14 @@ services:
 
   broadsea-run-dqd:
     profiles: [ "cdm-postprocessing", "dqd" ]
-    build: ./dqd
+    build: 
+      context: ./dqd
+      secrets:
+        - GITHUB_PAT
     platform: "linux/amd64"
     container_name: broadsea-run-dqd
     secrets:
       - CDM_CONNECTIONDETAILS_PASSWORD
-      - GITHUB_PAT
     volumes:
       - jdbc-drivers-data:/jdbc
       - cdm-postprocessing-data:/postprocessing
@@ -403,30 +390,7 @@ services:
       - ${DBT_PROJECT_PATH}:/usr/app
       - ${DBT_PROFILE_PATH}:/root/.dbt/
 
-  # broadsea-atlas-add-cdm:
-  #   profiles: [ "atlas-add-cdm" ]
-  #   build:
-  #     context: ./atlas/add_cdm
-  #   container_name: atlas-add-cdm
-  #   volumes:
-  #     - ./atlas/add_cdm/add_new_cdm.sh:/tmp/add_new_cdm.sh:ro
-  #     - ./atlas/add_cdm/new_cdm_template.json:/tmp/new_cdm_template.json:ro
-  #   entrypoint: ["sh", "/tmp/add_new_cdm.sh"]
-  #   secrets:
-  #     - ATLAS_NEW_CDMSOURCE_PASSWORD
-  #     - ATLAS_ADMIN_PASSWORD
-  #   environment:
-  #     NEW_CDMSOURCE_NAME: ${NEW_CDMSOURCE_NAME}
-  #     NEW_CDMSOURCE_KEY: ${NEW_CDMSOURCE_KEY}
-  #     NEW_CDMSOURCE_DIALECT: ${NEW_CDMSOURCE_DIALECT}
-  #     NEW_CDMSOURCE_CONNECTIONSTRING: ${NEW_CDMSOURCE_CONNECTIONSTRING}
-  #     NEW_CDMSOURCE_USERNAME: ${NEW_CDMSOURCE_USERNAME}
-  #     NEW_CDMSOURCE_CDMSCHEMA: ${NEW_CDMSOURCE_CDMSCHEMA}
-  #     NEW_CDMSOURCE_VOCABSCHEMA: ${NEW_CDMSOURCE_VOCABSCHEMA}
-  #     NEW_CDMSOURCE_RESULTSSCHEMA: ${NEW_CDMSOURCE_RESULTSSCHEMA}
-  #     HTTP_TYPE: ${HTTP_TYPE}
-  #     BROADSEA_HOST: ${BROADSEA_HOST}
-  #     ATLAS_ADMIN_USERNAME: ${ATLAS_ADMIN_USERNAME}
+
 
   ### Perseus
 
@@ -438,32 +402,20 @@ services:
     restart: unless-stopped
     volumes:
       - perseus-shareddb:/data/postgres
-
 
   perseus-files-manager:
     profiles: [ "perseus-files-manager", "perseus" ]
     image: perseushub/files-manager:latest
     platform: "linux/amd64"
     container_name: perseus-files-manager
     restart: unless-stopped
-    ports:
+    expose:
       - "10500:10500"
     environment:
       SPRING_PROFILES_ACTIVE: docker
       SPRING_DATASOURCE_URL: jdbc:postgresql://perseus-shareddb:5432/shared
-    #depends_on:
-    #  - perseus-shareddb
-
-
-  perseus-web:
-    profiles: [ "perseus-web", "perseus" ]
-    image: perseushub/web:latest
-    platform: linux/amd64
-    container_name: perseus-web
-    restart: always
-    labels:
-      - "traefik.enable=true"
-
+    depends_on:
+      - perseus-shareddb
 
   perseus-user:
     profiles: [ "perseus-user", "perseus" ]
@@ -479,12 +431,15 @@ services:
       USER_ENV: Docker
       TOKEN_SECRET_KEY: ${PERSEUS_TOKEN_SECRET_KEY}
       EMAIL_SECRET_KEY: ${PERSEUS_EMAIL_SECRET_KEY}
+      SERVER_ADDRESS: ${BROADSEA_HOST}
     volumes:
       - ./perseus/user/config.py:/app/config.py
-    ports:
+    expose:
       - "5001:5001"
-    #depends_on:
-    #  - perseus-shareddb
+    labels:
+      - "traefik.enable=true"
+    depends_on:
+      - perseus-shareddb
 
   perseus-backend:
     profiles: [ "perseus-backend", "perseus" ]
@@ -495,19 +450,21 @@ services:
       PERSEUS_ENV: Docker
     volumes:
       - ./perseus/backend/config.py:/app/config.py
-    ports:
+    expose:
       - "5004:5004"
-    #depends_on:
-    #  - perseus-shareddb
-    #  - perseus-files-manager
-
+    depends_on:
+      - perseus-shareddb
+      - perseus-files-manager
+  
   perseus-frontend:
     profiles: [ "perseus-frontend", "perseus" ]
     image: ohdsi/perseus-frontend:0.2.0
     platform: linux/amd64
     container_name: perseus-frontend
-    ports:
+    expose:
       - "4200:4200"
+    labels:
+      - "traefik.enable=true"
 
   perseus-vocabularydb:
     profiles: [ "perseus-vocabularydb", "perseus" ]
@@ -522,36 +479,36 @@ services:
     volumes:
       - perseus-vocabularydb:/data/postgres
       - ${PERSEUS_VOCAB_FILES_PATH}:/vocabulary
-    ports:
+    expose:
       - "5431:5432"
 
   perseus-cdm-builder:
     profiles: [ "perseus-cdm-builder", "perseus" ]
     image: perseushub/cdm-builder:latest
     platform: linux/amd64
     container_name: perseus-cdm-builder
-    ports:
+    expose:
       - "9000:9000"
     volumes:
       - ./perseus/cdm-builder/appsettings.Docker.json:/app/appsettings.Docker.json
     environment:
       - ASPNETCORE_ENVIRONMENT=Docker
-    #depends_on:
-    #  - perseus-shareddb
-    #  - perseus-files-manager
-    #  - perseus-vocabularydb
+    depends_on:
+      - perseus-shareddb
+      - perseus-files-manager
+      - perseus-vocabularydb
 
   perseus-solr:
     profiles: [ "perseus-solr", "perseus" ]
     image: perseushub/solr:latest
     platform: linux/amd64
     container_name: perseus-solr
-    ports:
+    expose:
       - "8983:8983"
     volumes:
       - perseus-solr:/var/solr
-    #depends_on:
-    #  - perseus-vocabularydb
+    depends_on:
+      - perseus-vocabularydb
 
   perseus-athena:
     profiles: [ "perseus-athena", "perseus" ]
@@ -562,10 +519,11 @@ services:
       ATHENA_ENV: Docker
     volumes:
       - ./perseus/athena/config.py:/app/config.py
-    ports:
+    expose:
       - "5002:5002"
-    #depends_on:
-    #  - perseus-solr
+    depends_on:
+      - perseus-solr
+
 
   perseus-usagi:
     profiles: [ "perseus-usagi", "perseus" ]
@@ -577,44 +535,44 @@ services:
       USAGI_ENV: Docker
     volumes:
       - ./perseus/usagi/config.py:/app/config.py
-    ports:
+    expose:
       - "5003:5003"
-    #depends_on:
-    #  - perseus-shareddb
-    #  - perseus-solr
+    depends_on:
+      - perseus-shareddb
+      - perseus-solr
 
   perseus-r-serve:
     profiles: [ "perseus-r-serve", "perseus" ]
     image: perseushub/r-serve:latest
     platform: linux/amd64
     container_name: perseus-r-serve
-    ports:
+    expose:
       - "6311:6311"
-    #depends_on:
-    #  - perseus-shareddb
+    depends_on:
+      - perseus-shareddb
 
   perseus-data-quality-dashboard:
     profiles: [ "perseus-dqd", "perseus" ]
     image: perseushub/data-quality-dashboard:latest
     platform: linux/amd64
     container_name: perseus-data-quality-dashboard
-    ports:
+    expose:
       - "8001:8001"
     environment:
       SPRING_PROFILES_ACTIVE: docker
       SPRING_DATASOURCE_URL: jdbc:postgresql://perseus-shareddb:5432/shared
       FILES_MANAGER_URL: http://perseus-files-manager:10500/files-manager
-    #depends_on:
-    #  - perseus-shareddb
-    #  - perseus-files-manager
-    #  - perseus-r-serve
+    depends_on:
+      - perseus-shareddb
+      - perseus-files-manager
+      - perseus-r-serve
 
   perseus-swagger:
     profiles: [ "perseus-swagger", "perseus" ]
     image: perseushub/swagger:latest
     platform: linux/amd64
     container_name: perseus-swagger
-    ports:
+    expose:
       - 8080:8080
 
   perseus-white-rabbit:
@@ -623,35 +581,15 @@ services:
     platform: "linux/amd64"
     container_name: perseus-white-rabbit
     restart: unless-stopped
-    ports:
+    expose:
       - "8000:8000"
     environment:
       SPRING_PROFILES_ACTIVE: docker
       SPRING_DATASOURCE_URL: jdbc:postgresql://perseus-shareddb:5432/shared
       files-manager-url: "http://perseus-files-manager:10500/files-manager"
-    #depends_on:
-    #  - perseus-shareddb
-    #  - perseus-files-manager
-
-
-  # broadsea-strategus:
-  #   profiles: [ "run-strategus" ]
-  #   build: 
-  #     context: ./strategus
-  #     args:
-  #       GITHUB_PAT: ${GITHUB_PAT}
-  #   platform: linux/arm64
-  #   container_name: broadsea-strategus
-  #   secrets:
-  #     - GITHUB_PAT
-  #     # - CDM_CONNECTIONDETAILS_PASSWORD
-  #     # - STRATEGUS_KEYRING_PASSWORD
-  #   environment:
-  #     RENV_PATHS_LIBRARY: /project/renv/library
-  #     INSTANTIATED_MODULES_FOLDER: /project/modules
-  #   volumes:
-  #     - ./strategus/execute.R:/project/execute.R
-  #   entrypoint: ["Rscript", "/project/execute.R" ]
+    depends_on:
+      - perseus-shareddb
+      - perseus-files-manager
 
 secrets:
   GITHUB_PAT:
@@ -693,10 +631,6 @@ secrets:
   WEBAPI_CDM_SNOWFLAKE_PRIVATE_KEY:
     file: ${WEBAPI_CDM_SNOWFLAKE_PRIVATE_KEY_FILE}
 
-  #ATLAS_NEW_CDMSOURCE_PASSWORD:
-  #  file: ${ATLAS_NEW_CDMSOURCE_PASSWORD_FILE}
-  #ATLAS_ADMIN_PASSWORD:
-  #  file: ${ATLAS_ADMIN_PASSWORD_FILE}